SMTL ID : 3dc8.1

Crystal structure of dihydropyrimidinase from Sinorhizobium meliloti

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: K.147, H.180, H.236 Ligands: ZN.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.180, A:H.236, H2O.5, H2O.17 ZN.2: 5 residues within 4Å: Chain A: H.56, H.58, K.147, D.313 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.56, A:H.58, A:D.313, H2O.17, H2O.21 ZN.7: 4 residues within 4Å: Chain B: K.147, H.180, H.236 Ligands: ZN.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.180, B:H.236, H2O.42, H2O.42 ZN.8: 5 residues within 4Å: Chain B: H.56, H.58, K.147, D.313 Ligands: ZN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.56, B:H.58, B:D.313, H2O.42 ZN.11: 4 residues within 4Å: Chain C: K.147, H.180, H.236 Ligands: ZN.12 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.180, C:H.236, H2O.56, H2O.68 ZN.12: 5 residues within 4Å: Chain C: H.56, H.58, K.147, D.313 Ligands: ZN.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.56, C:H.58, C:D.313, H2O.68, H2O.72 ZN.17: 4 residues within 4Å: Chain D: K.147, H.180, H.236 Ligands: ZN.18 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.180, D:H.236, H2O.94, H2O.94 ZN.18: 5 residues within 4Å: Chain D: H.56, H.58, K.147, D.313 Ligands: ZN.17 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.56, D:H.58, D:D.313, H2O.94

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 9 residues within 4Å: Chain A: N.144, G.174, A.175, L.176, I.372, P.454, F.455, P.456, S.459 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.176 Hydrogen bonds: A:F.455, A:S.459 Water bridges: A:S.459 ACT.9: 2 residues within 4Å: Chain B: Y.47, M.358 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.47 ACT.13: 9 residues within 4Å: Chain C: N.144, G.174, A.175, L.176, I.372, P.454, F.455, P.456, S.459 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.176 Hydrogen bonds: C:F.455, C:S.459 Water bridges: C:S.459 ACT.19: 2 residues within 4Å: Chain D: Y.47, M.358 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.47, D:Y.47

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: D.296, W.299, A.300, A.303, R.355 Chain B: K.252, G.253, W.465 Ligands: GOL.5 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.253, A:D.296, A:A.300, A:R.355, A:R.355 GOL.5: 9 residues within 4Å: Chain A: A.303, G.354, R.355 Chain B: G.253, R.255, A.461, L.462, W.465 Ligands: GOL.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:R.355, B:R.255 Hydrogen bonds: B:A.461 GOL.6: 9 residues within 4Å: Chain A: G.253, R.255, A.461, L.462, W.465 Chain B: A.303, G.354, R.355 Ligands: GOL.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.253, A:A.461, B:R.355 Water bridges: A:R.255 GOL.10: 8 residues within 4Å: Chain A: K.252, G.253, W.465 Chain B: D.296, W.299, A.300, R.355 Ligands: GOL.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.296, B:A.300, B:R.355, A:G.253 GOL.14: 9 residues within 4Å: Chain C: D.296, W.299, A.300, A.303, R.355 Chain D: K.252, G.253, W.465 Ligands: GOL.15 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.253, C:D.296, C:D.296, C:A.300, C:R.355, C:R.355 GOL.15: 9 residues within 4Å: Chain C: A.303, G.354, R.355 Chain D: G.253, R.255, A.461, L.462, W.465 Ligands: GOL.14 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.461 Water bridges: D:R.255, C:R.355 GOL.16: 9 residues within 4Å: Chain C: G.253, R.255, A.461, L.462, W.465 Chain D: A.303, G.354, R.355 Ligands: GOL.20 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.253, C:A.461, D:R.355 Water bridges: C:R.255 GOL.20: 8 residues within 4Å: Chain C: K.252, G.253, W.465 Chain D: D.296, W.299, A.300, R.355 Ligands: GOL.16 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.253, D:D.296, D:D.296, D:A.300, D:R.355

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Rodriguez, S. et al., Structure of dihydropyrimidinase from Sinorhizobium meliloti CECT4114: new features in an amidohydrolase family member. J.Struct.Biol. (2010)

Release Date

2009-04-21

Peptides

Dihydropyrimidinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dihydropyrimidinase